I had a +1 bonus to all my skills because I had a tier 2 destiny and a +2 bonus for a tier 3 destiny, now they are gone and have no clue why. I have tried levelling up, going to sleep and having a full fate/reckoning bar. Does anyone know what I've done wrong?
You only get those bonuses when using the "Jack-of-all-trades" style destinies, the ones that require skill points in all three branches. It sounds like you switched to a specialized 1 or 2 branch destiny, so you don't get that perk any more.